Post n.11 (English)
Hence the
biogenic elements (C, N, O, H) are the only ones which, through their
compounds, are adapted to carry out, in living organisms, the numerous
biological functions. We know that between these compounds the most
important are the Nucleic acid, DNA and RNA, and the
proteins.
The
proteins constitute tissues and organs, they permit the cells to communicate,
they control that which must enter and exit from the cell, they act as
antibodies.
All living
organisms have a complexity of independent functions which permit them:
nourishment, growth, reproduction, evolution, reaction to stimuli, death. All
these vital functions have in common the metabolism; that is that process of
chemical reactions which co-operate with proteins (enzymes)
which permit the living organisms to function. Inside the cell thousands of
enzymes can be found which rule and program thousands of chemical reactions. No
biological reaction and none of the functions mentioned above can happen
without their intervention, not even the synthesis of the nucleic acids.
The
proteins are macromolecules whose constituents are the amino acids.
But the
amino acids, in the prebiotic era, were present in our planet?
In 1953 S.
L. Miller, made the hypothesis of a primordial atmosphere made up CH4,
NH3, H2O, H2, succeeded, applying electrical
energy, in obtaining various organic substances and, among these, many amino
acids of which components of our proteins. This experiment, carried out in
plausible prebiotic conditions, marked the date of the birth of prebiotic
chemistry.
In the
years which followed various researchers have performed experiments both by
varying the composition of the gas mixture and the sources of energy. All these
studies have confirmed that in the prebiotic era, on our planet, the synthesis
of a large number of organic substances was possible, and among these, amino
acids were often present. Through those experiments was demonstrated the
presence, in the prebiotic era, of about 60 different amino acids. Moreover
also the presence of cyan hydric acid (HCN) precedent of purine, of formic
aldehyde (HCHO) precedent of ribose and
of other important organic substances among which urea have been demonstrated.
It is
remarkable that the same substances, in particular the amino acids, were found
in the meteorites going back to the era of the formation of our solar system.
The discovery of the amino acids in Miller’s experiments and their presence in
the meteorites demonstrates, according to scientists, the ease of synthesis of
these compounds. Even the sustainers of the “RNA World”
have no doubts on the presence of amino acids in the prebiotic era. Manfred
Eigen, referring to experiments like Miller’s, in “Gradini verso la vita” 1992,
affirms: «That which renders significant these experiments is not so much the
fact that in general amino acids form, but their relative frequency corresponds
to those that one meets in nature, and in particular in organic compounds discovered
in the meteorites».
At the
beginning of the 90’s, some research workers expressed doubt about the presence
of a primordial atmosphere made up of CH4, NH3, H2O,
H2. These research workers have supposed a primordial atmosphere
made up of CO2, N2 and H2O, and in such
conditions the formation of the amino acids with application of energy does not
take place. Miller has defined these studies hypotheses without sustaining
data.
No serious
research has doubted of the presence of amino acids in the prebiotic era.
We can
conclude that numerous and strong indications demonstrate the presence of amino
acids in the prebiotic era. From the synthesis of these molecules the proteins
have their origin.
But why the
amino acids? And again, are other solutions possible?
According
to my knowledge, in 60 years of prebiotic chemistry, the only scientist who
tried to give an answer to these questions was Mario Ageno in “Lezioni di
biofisica 3” 1984.
Prof. Mario
Ageno starts with the ascertainment that
the cells of living organisms do not contain molecules of intermediate
dimensions, but they are made up of:
a) Little
molecules as much possible simple, which can be found already in the ambiance,
or are easy to synthesize.
b) Linear
polymers (macromolecules) realized by repetitive operation as a limited number
of small molecules (monomers).
As it is
known the linear polymers can be obtained both by polyaddition
and by polycondensation.
The polyaddition is obtained by the union
of thousands but also millions of molecules of the
same type. It is the repetition of the same motive without any content of
information, it causes polymers usually of the linear type, for example polyethylene,
and it takes place through a chemical process fairly complex.
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| it.wikipedia.org/wiki/Polietilene |
The
polycondensation can happen between different molecules, through the
elimination of water molecules. This type of polymerization cannot take place
in the presence of water; however the chemical process is much more simple than
the polyaddition. It can lead to plastic material, but it is used by living
organisms for the construction of the macromolecules necessary to life. In
fact, as they are not the monotonous repetition of the same motive, the
polymers which result can contain information.
According
to Ageno the choice of the linear polymers has a constructive logic of its own.
Starting with a limited number of pieces, always with the same constructive
operation, molecular structures different but all connected between them are
realized. Probably there exists other solutions to accumulate informations and
functions but they are all very complicated. The most convenient solution from
an evolution point of view seems to be really that of the linear polymers. In
the end chemical evolution has chosen the polymeric process the most simple,
the polycondensation, and the simplest polymers that is linear polymers and
Ageno adds: «Hence it seems very probable that, wherever they appear under the impulse
of natural causes systems, in a way similar for their general characteristics
to living organisms which we know, these systems are based for their
reproduction, on some species of linear polymers. At the end, this solution can
be attained more easily and before any other in the course of a chemical
evolution which begins (this is inevitable) with small molecules made up of
very few atoms. And hence, what monomers once accepted the solution of linear polymers?».
Ageno examining the constituents of the
proteins asks himself the question: «What can be imagined more simple than an
amino acid, as structural element of a
linear polymer?». It is essentially a Carbon atom which establishes a bond with
the most simple of elements, the H.
A second
bond takes place with the most simple of the basic function, -NH2. A
third link takes place with the simplest acid function, -COOH. In the end, the
fourth link takes place with a side chain (R) of a hydrocarbon simple or with one of its derivates. Ageno concludes,
that the ease with which they are found in nature, for example in meteorites,
demonstrates that it is a question of simple molecules and which are easy to
synthesize, and they suggest the conclusion that polypeptide chains represent
the simplest solution.
 |
| it.wikipedia.org/wiki/Amminoacido |
Hence, to
the question: why the amino acid? The answer: because they are simple and easy
to synthesize.
Now the
question is that the amino acids are yes simple and easy to synthesize, but
they present a complex of properties without which life could not exist. Such
complexity confronts us with, as we shall see, a difficult question on the
problem of the origin of life, which normally does not fall in the ambiance of
physical science.
When Ageno
speaks of linear polymers, he refers to the primary structure
that is to the disposition and to the structure of the amino acids in the
polymer chain. The fact is that if the primary structure remained such, that is
in all simplicity a long polymer, it would not perform any vital function. In
reality the single proteins, over and above the primary structure, present a
secondary structure and a tertiary structure. The proteins perform their vital
functions only by having recourse to the secondary and tertiary structures.
To
understand how such new structures are possible, it is necessary to examine the
properties of amino acids.
1) The
first characteristic of amino acids is exactly that of being simple molecules
and easy to synthesize in a prebiotic ambiance.
2) A second
property is that amino acids are soluble in water and stable. If they were not
soluble in water, life would not exist, because they would have grouped
together like piece of tar or like large oily stains at the surface of the
water basins.
3) Miller’s
experiments have shown the presence, in the prebiotic era, of about 60
different amino acids, but life uses only 20. If these could have reacted in
water they would have given origin to an enormous number of polypeptides, of casual
composition and length, but of no interest for the origin of life. Hence the
amino acids must be soluble in water but they must not react in water. And in
fact they form polymers through the polycondensation which in water is not
permitted.
4) The
peptide bond is a link which is realized between the group –COOH of an
amino acid and the group –NH2 of another
amino acid with the elimination of a molecule of H2O. The
characteristic of this link is that it is a link in resonance. That is the double link between the Carbon atom and
Oxygen is not situated between the two atoms but it is distributed also on the
link C-N. The consequence of this delocalization is that every zone on the
peptide bond of the protein lies on a plane and the molecule of the protein cannot rotate around the peptide bonds. As we have said,
the
proteins are not
only long linear chains of amino acids.
This is only what is called a primary structure.
 |
| biochimica.bio.uniroma1.it |
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| www.unitus.it |
only long linear chains of amino acids.
This is only what is called a primary structure.
The single proteins present a secondary structure and a tertiary structure through which they
perform their vital functions. In the secondary structure they realize helical
structures and pleated sheet structures, α-helix and β-pleated sheet. Well, so
that these structures ca be realized, one necessary condition is that one
prevents the rotation of the molecule around the peptide bond.
The delocalization of the peptide bond prevents exactly such a rotation.
5) A second
condition so that these secondary structures can realize themselves is that the
constituent molecules be asymmetrical. We know that the amino acids, except for
Glycine, are chiral symmetry, that is they exist in two
forms asymmetrical one the mirror image of the other, called D and L.
Symmetrical
molecules cannot realize either α helix or β pleated sheet. The
secondary structures of the proteins can be realized by choosing one of the two asymmetrical forms. In the
livings organisms the form L was chosen.
6) Another
important characteristic of the peptide link is the presence of an atom of
Hydrogen linked to azote. The link between these two
elements gives origin to -Hδ+. As
we can see in the image of the α helix, broken line, -Hδ+ links to
the -CO δ- of another amino acid and
it is these links which stabilize
α helix. Without these links the secondary structure of the proteins
could not exist.
7 ) To
conclude, we have seen that in the amino acids Carbon is linked to a R side-chain.
These
side-chains are not chosen by chance. Some of these are hydrophilic, mixable
with water, others are hydrophobic not
mixable with water. In the tertiary structure of the protein, that is the globular structure the R hydrophobic concentrates
inside and the R hydrophilic in the external part. The final result is that the
protein results very stable and it is defended from the bios-project.blogspot.com
degradation of water.
degradation of water.
It is known
that the compounds in organic chemistry are about 1,5 million and grouped in
families. There does not exist another family of organic compounds which
presents likewise characteristics: the amino acids are unique, the passage was obliged.
One could
conclude that the amino acids are versatile. But we have before us life and, if
we wish to try to understand its origin, to the initial question: why the amino
acids?
The answer
that they are simple and easy to synthesize is not enough; because in reality
they must possess the following characteristics:
1) Simple
and easy to synthesize
2) Soluble
and stable in water
3) They
must not react in water
4) They
must link between each other giving origin to a peptide bond in resonance.
5) They
must be chiral
6) They
must contain a -Hδ+ residue on the atom of azote
7) The R
side-chain is not casual
If only one
of these properties were missing, we do not know how life would have been or
perhaps it would not exist. Amino acids are unique compounds.
And so the
question is: but how is it possible for the amino acids to have all these
properties, just there in these compounds unique, simple and easy to synthesize,
exactly those properties necessary to life, when life is still becoming?
Seven
strokes of luck?
Giovanni
Occhipinti
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